DETAILED CORRESPONDENCE
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
This action is in response to the papers filed February 10, 2026. Currently, claims 1, 3, 5-18 are pending.
All arguments have been thoroughly reviewed but are deemed non-persuasive for the reasons which follow. This action is made FINAL.
Any objections and rejections not reiterated below are hereby withdrawn.
Priority
This application claims priority to
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Drawings
The drawings are acceptable.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
Claims 11, and 14 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claims 11 and 14 contain trademark/trade names, namely fluorinert (FC-40). Where a trademark or trade name is used in a claim as a limitation to identify or describe a particular material or product, the claim does not comply with the requirements of 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph. See Ex parte Simpson, 218 USPQ 1020 (Bd. App. 1982). The claim scope is uncertain since the trademark or trade name cannot be used properly to identify any particular material or product. A trademark or trade name is used to identify a source of goods, and not the goods themselves. Thus, a trademark or trade name does not identify or describe the goods associated with the trademark or trade name. In the present case, the trademark/trade name is used to identify/describe a perfluorinated liquid and, accordingly, the identification/description is indefinite.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 1, 3, 5-10, 12-13, 15, 17-18 is/are rejected under 35 U.S.C. 103 as being unpatentable over Cao et al. (Characterizing the temporal dynamics of gene expression in single cells with sci-fate, bioRxiv preprint, posted June 11, 2019) in view of Herzog et al. (Protocol Exchange, Thiol-linked alkylation sequencing of RNA (SLAMseq), 2018).
Cao teaches a method for labeling newly synthesized mRNA with 4-thiouridine (S4U) with single cell combinatorial indexing (RNA-seq). Cells are incubated with S4U to label newly synthesized RNA. The cells are then treated with a thiol9SH)-linked alkylation reaction which covalently attaches a carboxyamidomethyl group to S4U, namely IAA (page 3). Cao teaches a well-specific barcode and degenerate unique molecular identifier (UMI) was used to identify guanine rather than adenine incorporations (page 3). Cao teaches UMI counts for the genes were determined.
With respect to Claim 3, Cao teaches 200uM S4U was used (page 23, para 2).
With respect to Claim 5, the IAA was 100mM (page 23, para 3).
With respect to Claim 6, the analysis was performed in wells. Cells were distributed into 96-well plates and mixed with primer and an “index”. The plates were then placed on ice (page 23, lines 27-32).
With respect to Claims 7 and 12, Cao teaches contacting with IAA is at 50C for 15 minutes.
With respect to Claim 8, the S4U treatment was performed for 2 hours.
With respect to Claim 9, Cao teaches using a reagent with IAA and DMSO.
With respect to Claim 13, Cao teaches the nucleic acids are placed on ice (page 23, lines 32) and then incubated at room temperature for 5 minutes (page 24, lines 8-9). While Cao does not teach the contacting is for 10 min each, this is mere routine optimization of routine conditions. The ordinary artisan would have been motivated to tweek the working conditions for the assays to obtain the best results.
With respect to Claim 15, 18, Cao teaches each well was then purified using AMPure XP beads. These beads are magnetic.
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Cao does not teach lysing cells and contacting with beads prior to treatment with IAA.
However, Herzog teaches a method of thiol-linked alkylation for the metabolic sequencing of RNA. Herzog teaches cells are treated with S4U and then the cells are lysed to isolate the RNA. The total RNA is then treated with iodoacetaminde treatment at 50C for 15 minutes before preparing a library and analysis of C and T generated sequences. Herzog teaches IAA treatment is performed after cell lysis. Herzog teaches S4U was used at a concentration of 100uM. Herzog teaches the IAA final concentration was 10mM (limitations of Claim 5). Herzog also teaches DMSO was added to the IAA reagent. The IAA contacting occurs for 15 minutes at 50C (limitations of Claim 7, 12).
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Therefore, it would have been prima facie obvious prior to the effective filing date of the claimed invention to have modified the S4U RNA method of Cao to lyse cells and contact nucleic acids with beads prior to treatment with IAA, as taught by Herzog. The prior art teaches the IAA treatment for modifying nucleotides for detection may occur in situ or on extracted nucleic acids. The ordinary artisan would have realized that the order of the steps for treatment with IAA may be performed before lysis of cells or after lysis of cells with the same expected result.
Claims 16, is/are rejected under 35 U.S.C. 103 as being unpatentable over Cao et al. (Characterizing the temporal dynamics of gene expression in single cells with sci-fate, bioRxiv preprint, posted June 11, 2019) in view of Herzog et al. (Protocol Exchange, Thiol-linked alkylation sequencing of RNA (SLAMseq), 2018) as applied to Claims 1, 3, 5-10, 12-13, 15, 17-18 above and further in view of Yuan et al. (Genome Biology, Vol. 19, No. 227, 2018).
Neither Cao nor Herzog teaches performing the analysis on a microfluidic chip.
However Yuan teaches SCOPE-Seq for linking live cell imaging and single-cell RNA sequencing. Yuan teaches barcoding mRNA capture beads in a microwell array system. The beads are conjugated to oligonucleotides with a cell-identifying sequencing barcode and a 3’ poly (dT) (page 1, col. 2). The beads thus comprise a UMI (see Figure 1 B). Yuan teaches on chip cell lysis, mRNA capture and reverse transcription to generate CPR-amplifiable, sequence barcoded cDNA attached to a bead (page 3, col. 1). Yuan teaches the method is economical and will serve as a powerful tool for connecting high-throughput microscopy and sequencing on multiple scales (page 5, col. 1).
Therefore, it would have been prima facie obvious prior to the effective filing date of the claimed invention to have modified the method of Cao in view of Herzog to substitute a microfluidic chip for the 96-well plate of Cao for the expected benefits taught by Yuan. Yuan specifically teaches the use of the microfluidic method is economical and will serve as a powerful tool for connecting high-throughput microscopy and sequencing on multiple scales (page 5, col. 1).
Conclusion
No claims allowable over the art.
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure.
Yuan et al. (Genome Biology, Vol. 19, No. 227, 2018) teaches SCOPE-Seq: a scalable technology for linking live cell imaging and single-cell RNA sequencing. Yuan illustrates in Figure 1, workflow for SCOPE-Seq that involve single-cell imaging with bead suspensions on a solid support followed by sequencing.
Erhard et al. (Nature Letter, Vol. 571, pages 419-423, 2019 with supplemental figures). Erhard teaches single cell RNA sequencing (scSLAM-seq). Erhard teaches scSLAM-seq involves briefly exposing cells to the nucleoside analogue 4-thiouridine (4sU). 4sU is then incorporated into new RNA during transcription and converted to a cytosine analogue using iodacetamide (IAA) before RNA sequencing (page 419, col. 1).
Duffy et al. (Curr Protoc Chem Biol. Vol. 8, No. 4, pages 234-250, December 7, 2017) teaches metabolic labeling of cellular RNA is a useful approach to study RNA biology. Duffy teaches S4U is a convenient nucleoside for metabolic labeling because it is cell-permeable, incorporated into newly transcribed RNA (abstract). The S4U RNA activated disulfide methane thiosulfonate conjugated biotin (MTS-biotin) followed by enrichment on streptavidin beads. Duffy teaches cells are cultured and 4-thiouridine nucleoside is added to the cell culture media (page 234). S4U was used at a concentration of as low as 100uM for 1.5-2 hours. Labeling is stopped by removing media and lysing the cells in TRIzol (page 234). The S4U RNA is reacted with activated sidulfide conjugated to biotin which biotinylates S4U. The biotinylated RNA is then enriched on streptavidin coated magnetic bead (page 235). The beads are collected and the samples are prepared for sequencing. Duffy teaches the metabolic labeling is performed in 6-well plates (page 5).
Hendriks et al. (Nature Communications, Vol. 10, No. 3138, 2019) teaches detection of 4sU-mediated base conversion in single cells. Figure 1a illustrates the NASC-seq methodology that performs alkylation on RNAs immobilized on beads for construction of libraries (page 3). Hendriks teaches bulk RNA alkylation was performed with 500uM 4sU for 3 hours. Total RNA was treated with IAA at 50C for 15 min, ph 8.0, 10mM IAA and 50% DMSO (pages 6-7).
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JEANINE ANNE GOLDBERG whose telephone number is (571)272-0743. The examiner can normally be reached Monday-Friday 6am-3:30pm.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Wu-Cheng (Winston) Shen can be reached on (571) 272-3157. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/JEANINE A GOLDBERG/Primary Examiner, Art Unit 1682
April 24, 2026
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